liggghts for beginner

Hi Everyone,

I'm pretty new to liggghts and having trouble on understanding and finding out some of the terms such as what is KinEng and rke in the terminal or liggghts log? (where can i find this info?)

I'm currently building DEM granular model with lattice model. and turns out that for some reason the KinEng & rke return as -Nan. during the run.

It is suspected that due to overlapping integration between lattice section and "fix integr all nve/sphere" (line64).

Please help

thank you in advance

code:

#Conveyor
atom_style granular
atom_modify map array
boundary p m m
newton off

communicate single vel yes

units si

region reg block 0 0.392 -0 0.0625 -0 0.380 units box #create boundary box (xmin xmax, ymin ymax, zmin zmax) zmax increase to 2 times as we need to do a target volume fraction of 0.6 to 0.3
create_box 1 reg

neighbor 0.01 bin
neigh_modify delay 0

#Material properties required for new pair styles
fix m1 all property/global youngsModulus peratomtype 5.e6
fix m2 all property/global poissonsRatio peratomtype 0.45
fix m3 all property/global coefficientRestitution peratomtypepair 1 0.3
fix m4 all property/global coefficientFriction peratomtypepair 1 0.5

#New pair style
pair_style gran model hertz tangential history #Hertzian without cohesion
pair_coeff * *

#Definition of TimeStep
timestep 0.00001 #timestep = 0.0001 second; each iteration step represents 0.00001 secs.

#Define Gravity
fix gravi all gravity 9.81 vector 0.0 0.0 -1.0 #vector x y z

#Boundary Definition
#shearing walls and shear movement in yplane
#fix shearwallx1 all wall/gran model hertz tangential history primitive type 1 xplane 0.392
fix shearwally1 all wall/gran model hertz tangential history primitive type 1 yplane 0.0625 shear x -1
fix shearwallz1 all wall/gran model hertz tangential history primitive type 1 zplane 0
#fix shearwallx2 all wall/gran model hertz tangential history primitive type 1 xplane 0
fix shearwally2 all wall/gran model hertz tangential history primitive type 1 yplane 0 shear x 1
fix shearwallz2 all wall/gran model hertz tangential history primitive type 1 zplane 0.380

#input particle radius
variable radius equal 0.003

#Particle Distributions for insertion
fix pts1 all particletemplate/sphere 15485863 atom_type 1 density constant 2500 radius constant ${radius}

fix pdd1 all particledistribution/discrete 32452843 1 pts1 1.0

#region for insertion
group nve_group region reg

#insert particle
fix ins all insert/pack seed 32452867 distributiontemplate pdd1 insert_every once overlapcheck yes volumefraction_region 0.3 region reg ntry_mc 10000

#apply nve integration to all particles that are inserted as single particles
fix integr all nve/sphere

#output settings, include total thermal energy
fix ts all check/timestep/gran 1000 0.1 0.1
compute rke all erotate/sphere
thermo_style custom step atoms ke c_rke f_ts[1] f_ts[2] vol
thermo 1000
thermo_modify lost ignore norm no

#insert the first particles so that dump is not empty
run 1 #initial step of run
dump dmp all custom/vtk 400 post/Test6_*.vtk id type type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius

#insert particles
run 1400 upto #number of timestep we simulate)
unfix ins

#Create Variable Input for Lattice
variable Lsimu equal 0.392
variable Dsimu equal 0.0625
variable Hsimu equal 0.1
variable Confining equal 1000 #vertical stress of lattice 1 kPa

lattice hcp ${radius} origin 0 0 ${radius}

variable tetraheight equal 0.8*${radius}

variable loc2 equal ${Hsimu}-${tetraheight}

region latreg block -0 ${Lsimu} -0 ${Dsimu} ${loc2} ${Hsimu} units box

create_atoms 1 region latreg #creating lattice particle
set region latreg density 2500 diameter 0.003 #size of lattice particle (input)
group top region latreg

variable topforcevert equal -${Confining}*${Lsimu}*${Dsimu}/count(top)

#neigh_modify exclude type 2 2

fix toprig all rigid group 1 top force * off off on torque * off off off
fix topforce top addforce 0.0 0.0 ${topforcevert}

#run after putting cap on top
run 2000 upto #number of timestep we simulate)